9RGE | pdb_00009rge

CryoEM structure of human alpha1beta3gamma2 GABA(A)R in complex with GARLH4 and the Neuroligin2 transmembrane helix, in CL47a

PDB DOI: https://doi.org/10.2210/pdb9RGE/pdb
EM Map EMD-53949: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-06-06 Released: 2026-06-17
Deposition Author(s): Kasaragod, V.B., Aricescu, A.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Molecular Biology Organization (EMBO), H2020 Marie Curie Actions of the European Commission, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structure of human alpha1beta3gamma2 GABA(A)R in complex with GARLH4 and the TMD of Neuroligin2, in CL47a

Kasaragod, V.B., Aricescu, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 275.6 kDa
Atom Count: 16,281
Modeled Residue Count: 1,920
Deposited Residue Count: 2,313
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-1	A, D	405	Homo sapiens	Mutation(s): 0 Gene Names: GABRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P14867 (Homo sapiens) Explore P14867 Go to UniProtKB: P14867
PHAROS: P14867 GTEx: ENSG00000022355
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14867
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P14867-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	B, E	439	Homo sapiens	Mutation(s): 0 Gene Names: GABRB3
UniProt & NIH Common Fund Data Resources
Find proteins for P28472 (Homo sapiens) Explore P28472 Go to UniProtKB: P28472
PHAROS: P28472 GTEx: ENSG00000166206
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28472
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit gamma-2	C	411	Homo sapiens	Mutation(s): 0 Gene Names: GABRG2
UniProt & NIH Common Fund Data Resources
Find proteins for P18507 (Homo sapiens) Explore P18507 Go to UniProtKB: P18507
PHAROS: P18507 GTEx: ENSG00000113327
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18507
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroligin-2	F [auth H]	29	Homo sapiens	Mutation(s): 0 Gene Names: NLGN2, KIAA1366
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFZ4 (Homo sapiens) Explore Q8NFZ4 Go to UniProtKB: Q8NFZ4
PHAROS: Q8NFZ4 GTEx: ENSG00000169992
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NFZ4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LHFPL tetraspan subfamily member 4 protein	G [auth L]	185	Homo sapiens	Mutation(s): 0 Gene Names: LHFPL4, GARLH4
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7J7 (Homo sapiens) Explore Q7Z7J7 Go to UniProtKB: Q7Z7J7
PHAROS: Q7Z7J7 GTEx: ENSG00000156959
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Z7J7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F]	10		N-Glycosylation	Interactions Focus chain H [auth F] Interactions & Density Focus chain H [auth F]

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G], L [auth K]	6		N/A	Interactions Focus chain I [auth G] Focus chain L [auth K] Interactions & Density Focus chain I [auth G] Focus chain L [auth K]

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], M	2		N/A	Interactions Focus chain J [auth I] Focus chain M Interactions & Density Focus chain J [auth I] Focus chain M

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J]	4		N/A	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW Query on PGW Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
PIO Query on PIO Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain N [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain N [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain N [auth A]	CA [auth D], N [auth A]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain CA [auth D] Focus chain N [auth A] Interactions & Density Focus chain CA [auth D] Focus chain N [auth A]
CLR (Subject of Investigation/LOI) Query on CLR Download:Ideal Coordinates CCD File SDF format, chain DA [auth L] MOL2 format, chain DA [auth L] mmCIF format, chain DA [auth L]	DA [auth L]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain DA [auth L] Interactions & Density Focus chain DA [auth L]
P1L Query on P1L Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	W [auth C], X [auth C], Y [auth C]	S-PALMITOYL-L-CYSTEINE C₁₉ H₃₇ N O₃ S FRAMWPHPFIXRCP-KRWDZBQOSA-N		Interactions Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
R16 Query on R16 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain Z [auth D] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth D]	T [auth B], Z [auth D]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Focus chain Z [auth D] Interactions & Density Focus chain T [auth B] Focus chain Z [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain AA [auth D]	AA [auth D]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Interactions & Density Focus chain AA [auth D]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain U [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain U [auth B]	BA [auth D], P [auth A], Q [auth A], R [auth A], U [auth B]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth B] Interactions & Density Focus chain BA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4
MODEL REFINEMENT	PHENIX	1.21

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-17

Deposition Author(s):

Kasaragod, V.B.

Aricescu, A.R.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/15
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L009609/1
European Molecular Biology Organization (EMBO)	European Union	ALTF137-2019
H2020 Marie Curie Actions of the European Commission	European Union	GABAARComp-897707
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_EX_MR/T046279/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01-GM135550
National Science Foundation (NSF, United States)	United States	NeuroNex 2014862